| dc.description.abstract | Plant health is not only determined by the plant itself, but also by its interaction with the
surrounding microbial environment. These communities comprise various microbes, including
bacteria and fungi, that inhabit different niches, such as the rhizosphere, endosphere, and
phyllosphere. They help regulate various functions, including nutrient cycling, hormone balance,
and stress tolerance, yet they are influenced by environmental drivers such as water availability,
temperature, and soil chemistry. Drought, in particular, thins water films, alters diffusion and
exudation, and reassembles microbial networks, with consequences for crop performance and
disease risk. Harnessing and studying beneficial microbes, therefore, requires not only an
ecological understanding of when and where communities shift, but also the use of tools and
techniques to detect, quantify, and track key taxa in complex plant-soil matrices.
Chapter 1 provides a review of previous literature, including peanut biology and drought
physiology, as well as plant growth-promoting rhizobacteria, with an emphasis on Paenibacillus.
It also discusses how moisture influences plant-associated microbiomes. Chapter 2 focuses on
designing and developing a qPCR tool for detecting the Paenibacillus reograndensis DH44 strain.
This strain has been researched for its potential as a biofertilizer in bermudagrass. Using K-mer
Exclusion by Cross-referencing (KEC) comparative genomics, we screened 1122 Paenibacillus
genomes, identifying unique regions in DH44 and designing two primer pairs: KEC12 and KEC13,
with primer efficiencies of 99.4% and 90.08%, respectively. The assay limit of detection was 124
cell copies per reaction and was successfully validated in planta, with qPCR signals closely
correlating with CFU plate count estimates. In chapter 3, we were able to distinguish the fungal
communities in peanut habitats (pegs, roots, and adjacent soil) under mid-season drought versus
irrigated treatment over three years (2022-2024), sampling both a drought-tolerant and a drought
sensitive variety at the Auburn University Plant Breeding Unit, Tallassee, AL. Water status and
habitat were the major differentiating factors, whereas variety effects were minimal as a main
effect and appeared primarily as an interaction with another factor. Mid-season drought resulted in
a modest change in overall diversity, but a clear variation in community composition, with the
pegs showing the most consistent separation over the years. Furthermore, the differential
abundance of peg tissue showed a shift toward stress-tolerant, endophytic lineages under drought
(e.g., Alternaria, Acremonium, Tilachlidium), while irrigation favored moisture-responsive and
opportunistic taxon profiles (Colletotrichum, Nothopassalora), underscoring water availability as
the dominant ecological filter of the peanut microbiome. Finally, Chapter 4 discusses the overall
conclusions and impacts. | en_US |
